Jiang Lab – Omics & AI for Regenerative Biology
Jiang Lab – Omics & AI for Regenerative Biology
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Our lab integrates RNA biology, multi-omics data, and artificial intelligence (AI) to investigate the spatial and temporal gene regulatory mechanisms that underlie development, regeneration, and disease. We develop and apply novel computational methods across diverse data modalities, including RNA-seq (bulk and single-cell), ATAC-seq, CLIP-seq, Ribo-seq, spatial transcriptomics, proteomics, metabolomics, and imaging. Through this integrative approach, we aim to reveal dynamic gene regulatory programs and interconnected molecular networks that shape cellular identity and drive tissue repair and degeneration diseases.
Selected Publications
Prabahar, A., Chamberlain, C.S., Vanderby, R., Murphy, W.L., Dangelo, W., Mangesh, K., Brown, B., Mazumder, B., Badylak, S. and Jiang, P. #, 2025. Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation. PLOS Computational Biology, 21(4), p.e1012997.
Chamberlain CS, Prabahar A, Kink JA, Mueller E, Li Y, Yopp S, Capitini CM, Hematti P, Murphy WL, Vanderby R, Jiang P#. Modulating the Mesenchymal Stromal Cell Microenvironment Alters Exosome RNA Content and Ligament Healing Capacity. (2024) Stem Cells. PubMed PMID: 38597671
Peng, Y., Toh, H., Clegg, D. and Jiang, P.#, (2025) AI-Enhanced Fluorescein Angiography Detection of Diabetes-Induced Silent Retinal Capillary Dropout and RNA-Seq Identification of Pre-Symptomatic Biomarkers. Biomedicines, 13(8), p.1926.
Prabahar A, Zamora R, Barclay D, Yin J, Ramamoorthy M, Bagheri A, Johnson SA, Badylak S, Vodovotz Y, Jiang P.#(2024) Unraveling the complex relationship between mRNA and protein abundances: a machine learning-based approach for imputing protein levels from RNA-seq data. NAR Genom Bioinform. PMCID: PMC10858678.
Sinha S, Sparks HD, Labit E, Robbins HN, Gowing K, Jaffer A, Kutluberk E, Arora R, Raredon MSB, Cao L, Swanson S, Jiang P, Hee O, Pope H, Workentine M, Todkar K, Sharma N, Bharadia S, Chockalingam K, de Almeida LGN, Adam M, Niklason L, Potter SS, Seifert AW, Dufour A, Gabriel V, Rosin NL, Stewart R, Muench G, McCorkell R, Matyas J, Biernaskie J. Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer. (2022). Cell. PMCID: PMC9888357.
Jiang, P.#, Chamberlain, C. S., Vanderby, R., Thomson, J. A., Stewart, R. (2020). TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes. Nucleic Acids Research.
Jiang, P., Nelson, J.D., Leng, N., Collins, M., Swanson, S., Dewey, C.N., Thomson, J.A. and Stewart, R. (2017) Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Dev Biol, 426, 143-154.
Roadmap Epigenomics Consortium (…Jiang P. …), Kundaje A. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
Leng, N., Chu, L.F., Barry, C., Li, Y., Choi, J., Li, X.M., Jiang, P., Stewart, R.M., Thomson, J.A. and Kendziorski, C. (2015) Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nature Methods, 12, 947-950.
Wang, F., Qi, Z., Yao, Y., Yu, G., Feng, T., Zhao, T., Xue, H.H., Zhao, Y., Jiang, P., Bao, L. and Yu, S., 2020. Exploring the stage-specific roles of Tcf-1 in T cell development and malignancy at single-cell resolution. Cellular & Molecular Immunology, pp.1-16.
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